Journal Club

Fall 2021 - Creative CRISPR

September 29: Organizational Meeting
Introductions, GTP advising committee, Program expectations, How to critique a paper, Selection of Fall topic.

October 6: Krypton Carolino (Winzeler Lab)
Muller et al. (2020) CiBER-Seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes. Science 370, eabb9662. [Journal] [PMC]

October 13: Carmine Chavez-Martinez (Zheng Lab)
Sun et al. (2020) Development of a CRISPR-SaCas9 system for projection- and function-specific gene editing in the rat brain. Science Advances 6, eaay6687. [Journal] [PMC]

October 20: Tiffany Chu (Muotri Lab)
Niu et al. (2017) Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 357, 1303-1307. [Journal] [PMC

October 27: Natalie DeForest (Majithia Lab)
Musunuru et al. (2021) In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in primates. Nature 593, 429-434. [Journal] [ReadCube

November 3: Jenna Kovsky (Sander Lab)
Hu et al. (2021) Co-opting regulation bypass repair as a gene-correction strategy for monogenic diseases. Molecular Therapy, In Press. Open Access: [Journal

November 10: Sara Elmasaouri (Yeo Lab)
Du et al. (2020) CRISPR artificial splicing factors. Nature Communications 11, 2973. Open Access: [Journal

November 17: Danielle Schafer (Yeo Lab)
Frangieh et al. (2021) Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion. Nature Genetics 53, 332–341. [Journal] [PMC]

November 24: Thanksgiving Holiday

December 1: Eleanora Rachtman (Bafna Lab)
Enache et al. (2020) Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nature Genetics 52, 662–668. [Journal] [PMC]

December 8: Faculty Panel. Professors Muotri, Signer, Simonson, and Winzeler.
Responsible Conduct of Research Discussion: Peer review ethics and standards.

Some resources:
JC Clements (2020) Don't be a prig in peer review. Nature [Journal]
M Picciotto (2020) Peer Review Week 2020: Trust in Peer Review. J. Neurosci. 40, 7378. [Journal]
DG Hamilton et al. (2020) Meta-Research: Journal policies and editors’ opinions on peer review. eLife 9:e62529 [Journal]
GENETICS (GSA) Peer Review Training Program. [Journal]
NIH Grants Peer Review Policies and Practices:

Select Winter topic.


Winter 2022 - Analysis of Failure

What can we learn about best practices from acknowledged errors? 

January 5: Chris Balak (Glass Lab)
Marcos et al. (2010) CXCR2 mediates NADPH oxidase–independent neutrophil extracellular trap formation in cystic fibrosis airway inflammation. Nature Medicine 16, 1018-1023. [paper] [retraction]

January 12: Lizmarie Garcia-Rivera (Wechler-Reya and Furnari Labs)
Schaeffer et al. (2017) Unexpected mutations after CRISPR–Cas9 editing in vivo. Nature Methods 14, 547–548. [paper]
Responses: Nutter et al. [response], Wilson et al. [response], Lescarbeau et al. [response], Lareau et al. [response], Kim et al. [response]
Retraction: [retraction notice

January 19: Maya Gosztyla (Yeo Lab)
Lim et al. (2014) 24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex. PLoS Genetics 10, e1004792. [paper] [expression of concern] [retraction]

January 26: Alyssa Holman (Chi and Engler Labs)
Conrad et al. (2008) Generation of pluripotent stem cells from adult human testis. Nature 456, 344–349. [paper] [erratum]
Ko et al. (2010) Human adult germline stem cells in question [brief communication arising] [reply]
Conrad et al. (2014) [retraction]

February 2: Pratibha Jagannatha (Yeo Lab)
Venters and Pugh (2013) Genomic organization of human transcription initiation complexes. Nature 502, 53-58. [paper]
Siebert and Söding (2014) Universality of core promoter elements? [brief communication arising]
Venters and Pugh (2014) [retraction]

February 9: Blair Jha (Ren Lab)
Maisonneuve et al. (2011) Bacterial persistence by RNA endonucleases. PNAS 108, 13206-13211. [paper] and (2018) PNAS 115, E2901. [retraction]

February 16: Rebecca Melton (Gaulton Lab)
Yi et al. (2013) Betatrophin: a hormone that controls pancreatic β cell proliferation. Cell 153, 747-758 [paper]; Gusarova et al. (2014) ANGPTL8/Betatrophin Does Not Control Pancreatic Beta Cell Expansion. Cell 159, 691-696 [paper]; Yi et al. (2014) [correspondence]; Cox et al. (2016) Resolving Discrepant Findings on ANGPTL8 in β-Cell Proliferation: A Collaborative Approach to Resolving the Betatrophin Controversy. PLoS ONE 11, e0159276. [paper]; Yi et al. (2017) Cell [retraction].

SPECIAL EVENT Thursday, February 17: 2022 Daniel T. O'Connor Memorial Lecture
Professor Nik Schork • 12 noon • Leichtag 107 and online [flyer]

February 23: Kween Agba (Zheng Lab)
Kanadia and Cepko (2010) Alternative splicing produces high levels of noncoding isoforms of bHLH transcription factors during development. Genes Dev 24, 229-234 [paper]
Prasov et al. (2010) A critical analysis of Atoh7 (Math5) mRNA Splicing in the developing mouse retina. PLoS ONE [paper]
Kanadia and Cepko (2011) Genes Dev 25, 1344 [retraction]

March 2: Faculty Panel. Professors Carlin, Engler, Farley, and Sander
Responsible Conduct of Research Discussion: Avoiding and correcting errors in research.

Select Spring quarter topic.


Spring 2022 - Rare disease genetics

March 30: Sam Hatch (Yeo Lab)
Kim et al. (2019) Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease. New Engl J Med 38, 1644-1652. [Journal] [PMC]

April 6: AJ Daniels (Signer and Bennett Labs)
Kumar et al. (2022) Oligonucleotide correction of an intronic TIMMDC1 variant in cells of patients with severe neurodegenerative disorder. npj Genom Med 7, 9. [Journal] [PMC]

April 13: Mitchell Kong (Simonson Lab)
Dias et al. (2016) BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription. Am J Hum Genet 99, 253-274 [Journal] [PMC]

April 20: Brittany Leger (Palmer Lab)
Wilson et al. (2021) Active site variants in STT3A cause a dominant type I congenital disorder of glycosylation with neuromusculoskeletal findings. Am J Hum Genet 108, 2130-2144. [Journal] [PubMed]

April 27: Rachel McMillen (Carlin and Benner Labs)
To et al. (2019) A Compendium of Genetic Modifiers of Mitochondrial Dysfunction Reveals Intra-organelle Buffering. Cell 179, 1222-1238. [Journal] [PMC]

May 4: Xiaomi Du (Majithia Lab)
Turro et al. (2020) Whole-genome sequencing of patients with rare diseases in a national health system. Nature 583, pages96–102 [Journal] [PMC] [preprint]

May 11: Mei Okino (Sander and Gaulton Labs)
Wali et al. (2020) Oxidative Stress-Induced Axon Fragmentation Is a Consequence of Reduced Axonal Transport in Hereditary Spastic Paraplegia SPAST Patient Neurons. Front. Neurosci. 14, 401. [Journal] [PMC]

May 18: Hannah Mummey (Gaulton Lab)
Koblan et al. (2021) In vivo base editing rescues Hutchinson–Gilford progeria syndrome in mice. Nature 589, 608-614. [Journal] [PMC

May 25: Michelle Ragsac (Farley Lab)
Horstick et al. (2013) Stac3 is a component of the excitation-contraction coupling machinery and mutated in Native American myopathy. Nat Commun 4, 1952. Open Access: [Journal] [PMC]

June 1: Mike Cuoco (Gage Lab)
Long et al. (2020) Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. Cell Stem Cell 27, 765-783.e14. [Journal] [PMC

June 8: Faculty Panel. Professors Cherqui, Chi, and Gleeson
Responsible Conduct of Research Discussion: Scientific ethics in therapeutics development for rare genetic disease.

Summer Book Club selection: Calling Bullshit (Bergstrom and West)